Variant report

Variant	rs72820479
Chromosome Location	chr2:48651595-48651596
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:48649466..48652347-chr2:48667979..48669728,2	K562	blood:
2	chr2:48649795..48653171-chr2:48665814..48667830,3	K562	blood:
3	chr2:48645150..48646743-chr2:48650153..48652145,2	MCF-7	breast:
4	chr2:48643733..48645696-chr2:48650632..48652708,2	K562	blood:
5	chr2:48541412..48543498-chr2:48651556..48653117,2	K562	blood:
6	chr2:48649540..48651703-chr2:48667084..48669876,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162869	Chromatin interaction
ENSG00000170802	Chromatin interaction
ENSG00000272663	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10208627	0.83[ASN][1000 genomes]
rs10211336	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10454133	0.99[ASN][1000 genomes]
rs10454134	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11680719	0.98[ASN][1000 genomes]
rs11683639	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11683708	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11689622	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12105983	0.83[ASN][1000 genomes]
rs13399936	0.99[ASN][1000 genomes]
rs13400909	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13401749	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13401752	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35913553	0.95[EUR][1000 genomes]
rs4274640	0.98[ASN][1000 genomes]
rs4316980	0.99[ASN][1000 genomes]
rs4438532	0.97[ASN][1000 genomes]
rs4494796	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4547570	0.93[EUR][1000 genomes]
rs4606978	0.97[ASN][1000 genomes]
rs4638844	0.92[ASN][1000 genomes]
rs55640438	0.97[ASN][1000 genomes]
rs55757090	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55971719	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56156294	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56365822	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58020097	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58969359	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58978223	0.86[ASN][1000 genomes]
rs59045263	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60042255	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60825643	0.95[EUR][1000 genomes]
rs60988618	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61303367	0.86[ASN][1000 genomes]
rs62137018	0.87[ASN][1000 genomes]
rs62137019	0.87[ASN][1000 genomes]
rs62137021	0.85[ASN][1000 genomes]
rs62137041	0.97[ASN][1000 genomes]
rs66705539	0.85[ASN][1000 genomes]
rs6732196	0.94[ASN][1000 genomes]
rs6735288	0.84[ASN][1000 genomes]
rs6747441	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6749773	0.87[ASN][1000 genomes]
rs72820454	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72820474	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72820484	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72820492	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72820494	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72820499	0.97[ASN][1000 genomes]
rs7565792	0.93[ASN][1000 genomes]
rs7568574	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2762252	chr2:48554150-48741093	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv581775	chr2:48619869-48714938	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv524919	chr2:48649738-48658779	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs72820479	PPP1R21	cis	Thyroid	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48647800-48651800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr2:48648000-48651600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr2:48648000-48655000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:48648200-48651600	Weak transcription	Brain Cingulate Gyrus	brain
5	chr2:48648400-48651600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr2:48648400-48651600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr2:48648400-48652400	Weak transcription	K562	blood
8	chr2:48650400-48652800	Enhancers	Brain Hippocampus Middle	brain
9	chr2:48650600-48651600	Weak transcription	HMEC	breast
10	chr2:48651000-48653400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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